Variant report

Variant	rs11880939
Chromosome Location	chr19:53099069-53099070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53073369..53074894-chr19:53098457..53100751,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF701-1	chr19:53098870-53100598	NONHSAT067565

Variant related genes	Relation type
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10401627	0.84[EUR][1000 genomes]
rs10403603	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420776	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11672999	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11878446	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880926	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11882538	0.91[ASN][1000 genomes]
rs11882556	0.89[ASN][1000 genomes]
rs11883366	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12979546	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12985245	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1802617	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2068066	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2068067	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2068068	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2126501	0.91[ASN][1000 genomes]
rs2169527	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169528	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279151	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279152	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35151776	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35379780	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4450518	0.90[ASN][1000 genomes]
rs4801920	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4801921	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4801922	0.92[ASN][1000 genomes]
rs4801923	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802975	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802976	0.90[ASN][1000 genomes]
rs60763836	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62117255	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62117256	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509653	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6509654	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6509655	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67036527	0.84[ASN][1000 genomes]
rs7245397	0.91[ASN][1000 genomes]
rs7247002	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247069	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250819	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254868	0.90[ASN][1000 genomes]
rs7259768	0.91[ASN][1000 genomes]
rs7259905	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259938	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7260315	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74176156	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110686	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8110794	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1805104	chr19:53090157-53100585	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv963070	chr19:53091108-53105222	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
14	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
15	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	esv2607292	chr19:53094426-53099769	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv3495535	chr19:53095063-53100229	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv828616	chr19:53095216-53137823	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
19	esv3384239	chr19:53095240-53099238	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv3409448	chr19:53095390-53099088	Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53074600-53103600	Weak transcription	Fetal Brain Male	brain
2	chr19:53087400-53103600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:53087600-53099400	Weak transcription	Brain Angular Gyrus	brain
4	chr19:53087600-53103600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:53088400-53103600	Weak transcription	Psoas Muscle	Psoas
6	chr19:53088600-53099200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:53088800-53103600	Weak transcription	Colon Smooth Muscle	Colon
8	chr19:53088800-53103600	Weak transcription	Right Ventricle	heart
9	chr19:53088800-53103800	Weak transcription	Right Atrium	heart
10	chr19:53089000-53103800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:53089400-53099400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:53089800-53100000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:53090800-53100000	Weak transcription	Fetal Brain Female	brain
14	chr19:53091000-53104200	Weak transcription	Spleen	Spleen
15	chr19:53091200-53099200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:53091200-53099400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:53091600-53099400	Weak transcription	HSMM	muscle
18	chr19:53092200-53103600	Weak transcription	Gastric	stomach
19	chr19:53094000-53099400	Weak transcription	Brain Germinal Matrix	brain
20	chr19:53094000-53103800	Weak transcription	Aorta	Aorta
21	chr19:53094200-53099400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:53095000-53103400	Weak transcription	Fetal Heart	heart
23	chr19:53095200-53099800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:53095600-53099200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:53095600-53099800	Weak transcription	NHLF	lung
26	chr19:53095800-53099200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:53095800-53099200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr19:53095800-53099400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:53096000-53099200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr19:53096000-53103600	Weak transcription	Pancreas	Pancrea
31	chr19:53096000-53103800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:53096000-53104000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:53096600-53102200	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr19:53097400-53100400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
35	chr19:53097600-53099400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:53097600-53100000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:53097600-53100000	ZNF genes & repeats	Thymus	Thymus
38	chr19:53097600-53100200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:53097600-53100200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:53097600-53100200	ZNF genes & repeats	Liver	Liver
41	chr19:53097600-53100400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
42	chr19:53097600-53100400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:53097600-53101000	Strong transcription	Dnd41	blood
44	chr19:53097600-53101200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:53097600-53101200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
46	chr19:53097600-53101200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr19:53097600-53102200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:53097800-53099800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:53097800-53100400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr19:53097800-53100600	Strong transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links